Solutions to Problems

Tips for solving common problems and errors

---

Allele Depth (AD) is lower than expected

AnalyzeCovariates fails with error message "RScript exited with 1"

Errors about contigs in BAM or VCF files not being properly ordered or sorted

Errors about input files having missing or incompatible contigs

Errors about misencoded quality scores

Errors about read group (RG) information

Errors in SAM/BAM files can be diagnosed with ValidateSamFile

I am unable to use VQSR (recalibration) to filter variants

I do not get the annotations I specified with -A

I expect to see a variant at a specific site, but it's not getting called

I need to run programs that require different versions of Java